Dhaval Patel

5 Questions 23 Answers 0 Followers

Questions related from Dhaval Patel

How to give restraint in terms of kcal/mol and 2.05 Ang in distance for a metal ion to Cpc ring in metallocene in gromacs?

Dear Friends, I am trying to simulate a metallocene ligand with a metal ion between two Cp rings (Refer image). For ff for metal ion and ligand I have generated using QM calc. Now I have...

08 August 2018 4,371 1 View

Does GROMACS support cp centroid (ferrocene- like mol) simulations?

Hi Everyone, I am interested in simulations of metallocenes in general Ferrocene like organometallic compounds. For parametrization of the ligand I will be using antechamber and amber utilities...

07 July 2018 5,859 2 View

Regarding conversion from amber (prmtop and inpcrd) to gromacs itp and gro?

Hi Everyone, I have a protein-Mn(ion)+ligand to simulate. I have taken the .dat and .prep files for Mn from an existing literature source and I am able to successfully convert in to prmtop and...

06 June 2018 2,293 6 View

How to perform gromacs MD simulations of a protein to get the atomistic details of its unfolding at different temperatures?

I want to perform a MD simulation of a protein at different temperature to check its stability and unfolding at different temperature (300K, 310K, 320K etc.).

06 June 2014 6,751 5 View

My protein of interest is of 39kDa and after purification with HIS tag, I am getting a single band at 60kDa. Why?

I have cloned a gene in pET15b, pET28a, pET30a and used BL21, Rossetta and pLysS cells for expression but after purification I get a single band at 60kDA . I have added BME in loading dye, so the...

04 April 2014 8,268 28 View